Bioconductor Packages

Supervised Non-negative Matrix Factorization for Dimensional Reduction in Single-Cell Analysis

Evaluate Cellspecific Mixing

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Reconstruction, visualization and analysis of branching trajectories

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Cepo for the identification of differentially stable genes

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Quantitative comparison of multiple ChIP-seq datasets

Quality metrics for ChIPseq data

ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

Identifying Protein Binding Sites in High-Throughput Sequencing Data

Simulation of ChIP-seq experiments

R interface to a subset of OpenBabel functionalities

Cheminformatics Toolkit for R

CHiCAGO: Capture Hi-C Analysis of Genomic Organization

Analysis of single-cell epigenomics datasets with a Shiny App

Infrastructure for Chromatographic Mass Spectrometry Data

End-to-End Analysis of Small RNA-Seq Data from Viroids

CiteFuse: multi-modal analysis of CITE-seq data

A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

Detect and Correct Genomic DNA Contamination in RNA-seq Data

Infers clonal composition of a tumor

Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise

Clustering of MS2 Spectra for Metabolite Identification

ClustAll: Data driven strategy to robustly identify stratification of patients within complex diseases

Clustering of Immune Receptor Repertoires

Calculate similarity of clusters from different single cell samples using foldchanges

Judging Quality of Clustering Methods using Mutual Information

The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data

Coordinated Gene Activity in Pattern Sets

Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets

Complexome Profiling Analysis package

Automated detection tool for spillover errors

Make Complex Heatmaps

Creating and Using (Chemical) Compound Annotation Databases

ConsensusClusterPlus

Create Copy-Number Plots using karyoploteR functionality

Helper files for CopywriteR

Coralysis sensitive identification of imbalanced cell types and states in single-cell data via multi-level integration

Classes and Functions to Serve as the Basis for Other 'Gx' Packages

Correlation Motif Fit

An R package for colorectal cancer screening and microbiome analysis

Tools for counting and visualising mutations in a target location

Queries the Human Cell Atlas

Power analysis for CyTOF experiments